A comparison of single‐sample effective size estimators using empirical toad (Bufo calamita) population data: genetic compensation and population size‐genetic diversity correlations

The accuracy and precision of four single‐sample estimators of effective population size, N_e (heterozygote excess, linkage disequilibrium, Bayesian partial likelihood and sibship analysis) were compared using empirical data (microsatellite genotypes) from multiple natterjack toad (Bufo calamita) populations in Britain (n = 16) and elsewhere in Europe (n = 10). Census size data were available for the British populations. Because toads have overlapping generations, all of these methods estimated the number of effective breeders N_b rather than N_e. The heterozygote excess method only provided results, without confidence limits, for nine of the British populations. Linkage disequilibrium gave estimates for 10 British populations, but only six had finite confidence limits. The Bayesian and sibship methods both produced estimates with finite confidence limits for all the populations. Although the Bayesian method was the most precise, on most criteria (insensitivity to locus number, correlation with other effective and census size estimates and correlation with genetic diversity) the sibship method performed best. The results also provided evidence of genetic compensation in natterjack toads, and highlighted how the relationship between effective size and genetic diversity can vary as a function of geographical scale.     

Effects of the 2003 heatwave and climatic warming on mollusc communities of the Saône: a large lowland river and of its two main tributaries (France)

The study of the dynamics of mollusc populations of the Saône and its two main tributaries, the Doubs and Ognon, over several years has provided us with the opportunity of highlighting the consequences of climatic warming and especially of the heatwave of 2003 on these organisms. From 1987 to 2003, the mean temperature of the waters of the Saône upstream of Lyon (Couzon) increased by 1.5°C. In addition, the summer of 2003 was the hottest since 1500 at least. We used correspondence analysis to identify structure change in mollusc data dating from September 1996 to December 2004. The results revealed: (1) during the period from September 1996 to July 2003, a significant progressive change in the mollusc community structure of the Saône upstream of Lyon, probably linked to the increase of temperature; (2) from July to August 2003 during the heatwave, a sudden change in the structure of mollusc communities and a significant decrease of species richness and density of gastropods and bivalves. During 2004, mollusc density and particularly that of Pisidium remained dramatically low. Similar observations were performed at four other sites along the Saône and in the lower reaches of its two main tributaries. This suggests that the resilience of the mollusc populations (i.e., the speed with which they return to a predisturbance state) to the heatwave is low. In this way, as different climatic models have predicted an increase in the frequency of summers as hot as that of 2003 during this century, more than half the mollusc species currently inhabiting the potamic area of the Saône, Doubs and Ognon, and probably other large rivers, are probably directly threatened with extinction.     

Transformation zone sampling rate is a useful performance indicator for practitioners collecting cervical samples using SurePathTM liquid-based cytology system

An analysis of the reports of 53 982 liquid-based cytology (LBC) samples processed at the Royal Victoria Infirmary, Newcastle, reveals a significant relationship between the transformation zone (TZ) sampling rate observed in specimens submitted from different practices and their overall detection rate for dyskaryosis. The observed correlation (R = 0.184; P = 0.033, CI = 0.017 to 0.397) is very similar to that described previously using conventional cervical smears and confirms the potential relevance of TZ sampling rates as an indicator of consistently effective specimen collection. The correlation between unsatisfactory sample rates and detection rates for high-grade dyskaryosis (R = -0.188, P = 0.030, CI = -0.865 to -0.045) also shows a significant relationship for LBC samples which was not previously seen in conventional smears. The essential role of smear taker feedback, the use of transformation zone sampling and unsatisfactory smear rates as key indicators and the practical issues relating to routine reporting of transformation zone components are discussed.     

Optimal Representation of Supplementary Variables in Biplots from Principal Component Analysis and Correspondence Analysis

This paper treats the topic of representing supplementary variables in biplots obtained by principal component analysis (PCA) and correspondence analysis (CA). We follow a geometrical approach where we minimize errors that are obtained when the scores of the PCA or CA solution are projected onto a vector that represents a supplementary variable. This paper shows that optimal directions for supplementary variables can be found by solving a regression problem, and justifies that earlier formulae from Gabriel are optimal in the least squares sense. We derive new results regarding the geometrical properties, goodness of fit statistics and the interpretation of supplementary variables. It is shown that supplementary variables can be represented by plotting their correlation coefficients with the axes of the biplot only when the proper type of scaling is used. We discuss supplementary variables in an ecological context and give illustrations with data from an environmental monitoring survey.     

Who is Who? Non-invasive Methods to Individually Sex and Mark Altricial Chicks

Many experiments require early determination of offspring''s sex as well as early marking of newborns for individual recognition. According to animal welfare guidelines, non-invasive techniques should be preferred whenever applicable. In our group, we work on different species of song birds in the lab and in the field, and we successfully apply non-invasive methods to sex and individually mark chicks. This paper presents a comprehensive non-invasive tool-box. Sexing birds prior to the expression of secondary sexual traits requires the collection of DNA-bearing material for PCR. We established a quick and easy method to sex birds of any age (post hatching) by extracting DNA from buccal swabs. Results can be obtained within 3 hours. For individual marking chick''s down feathers are trimmed in specific patterns allowing fast identification within the hatching order. This set of methods is easily applicable in a standard equipped lab and especially suitable for working in the field as no special equipment is required for sampling and storage. Handling of chicks is minimized and marking and sexing techniques are non-invasive thereby supporting the RRR-principle of animal welfare guidelines.     

Evaluating preservation medium for the storage of DNA in African lion Panthera leo faecal samples

Lion faecal samples, collected in the field between 1 hour to 1 week after defecation were preserved in three different media （ethanol, ASL buffer and Twostep storage）. The aim was to determine which faecal DNA field preservation method best enhances PCR amplification success. Samples stored in ethanol showed a significantly higher amplification success of microsat ellite loci than samples stored in the other two media. In contrast, amplification success of a mitochondrial locus was similar among the samples stored in the three types of media. We reviewed twelve previous studies that employed different media for the storage of faeces, although patterns of success were not fully consistent among different media, ethanol storage was scored high est in the majority of these tests     

重要值的改进及其在羊草群落分类中的应用

对重要值进行了改进, 首次提出了理论平均重要值(theoretical mean importance value, TMIV)、简化重要值(simple importance value, SIV)和样地指数(sample plot index, SPI)的概念。即, 理论平均重要值是指随物种数目变化样地内各种植物理论上的平均重要值。简化重要值是指理论平均重要值乘以某一植物的生物量与样地内所有植物的平均生物量的比值或者乘以某一植物的体积(盖度乘以高度)与样地内所有植物的平均体积的比值。样地指数是指简化重要值乘以某一植物的生物量与所有样地中该植物的平均生物量的比值或者乘以某一植物的体积与所有样地中该植物的平均体积的比值。相对重要值而言, 简化重要值减少了野外工作量。而样地指数既反映了物种在样地内所占有的优势, 又反映了物种在样地间所占有的优势, 使得不同样地的重要值更具可比性。文中用重要值、简化重要值和样地指数三个指标进行羊草群落的聚类分析, 结果表明, 简化重要值可用于植物群落的数量分类, 样地指数比重要值更适宜用于植物群落的数量分类。     

流溪河大型底栖动物群落的时空分布及其影响因子

流溪河位于我国热带与亚热带过渡区,其底栖动物种类丰富,群落的物种组成结构具有明显的区域性,掌握该地区的物种组成特征及与环境要素的关系是建立生态监测与评估方法的基础。于2018年的枯水期（3月、12月）和丰水期（6月、9月）,自流溪河上游至下游共计20个段面对底栖动物进行了定量采样,同时测定了相应的环境因子,采用多元统计方法对流溪河水环境与群落结构及其相关关系进行了分析。共检出底栖动物76个分类单元,隶属于7纲20目50科,其中水生昆虫相对丰度最高,占69.39%。在4个优势分类单元中,摇蚊族（Chironomini）相对丰度为20.19%,河蚬（Corbicula fluminea）、短沟蜷属的一种（Semisulcospira sp.1）、双突细蜉（Caenis bicornis）,相对丰度在7%-9%之间。底栖动物丰度和种类多样性均与浊度呈显著负相关;枯水期底栖动物丰度与总磷呈显著负相关,丰水期则呈显著正相关。在丰水期,不同河流级别上底栖动物群落具有明显的差异,表现较强的分布格局,而在枯水期这种分布格局不明显。典范对应分析（CCA）表明,在丰水期,影响或解释流溪河底栖动物群落变化的主要因子为pH、溶解氧、水温、电导率和硅酸盐,而在枯水期则为pH和硝态氮。受电站与采沙的影响,部分河段发生非自然断流和底质的显著改变,导致底质与水深等数据的异常变化,反映了人类活动对该河流生境与环境的重要影响。     

Enhancement of the MONERIS Model for Application in Alpine Catchments in Austria

Mountainous catchments are usually not in focus of the modelling of nutrient fluxes on catchment scale. Out of 9 model approaches tested in the EU‐project EUROHARP only MONERIS claims to be capable of modelling nitrogen and phosphorus emissions in a landscape with mountainous slope. Results derived in the present study indicate that the MONERIS 2.14 model in its current version is not able to reproduce the measured nutrient loads in rivers from alpine catchments in Austria with a size of 70 to 400 km². Despite this apparent limitation, MONERIS delivers a framework flexible enough to offer the possibility for the introduction of adaptations to regions that had not been a focus during its development. Significant improvements in model performance have been achieved during this study with relatively simple adaptations: (i) calibration a snowmelt constants, (ii) adaptation of the nitrogen balance for open and naturally covered areas, (iii) adaptation of the denitrification approach for groundwater of solid rock areas with low nitrogen surplus and high amount of leakage water, (iv) introduction of the differentiation of area‐specific suspended solids emission factors for mountainous open areas covered either with glaciers or not, (v) definition of new input parameters for phosphorus concentrations in solid limestone and schist/gneiss rocks and of dissolved phosphorus concentrations in surface runoff and groundwater flow for mountainous areas. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Some ecological aspects of aquatic oligochaetes in the Lower Pearl River (People's Republic of China)

Densities of the 8 most important species or genera of the 15 taxa found at a series of stations along the Guangzhou Reach of the Pearl River are given. Shannon-Weaver diversity index values were low throughout the area studied. No clear correlations were found between oligochaetes and NH₃-N or a combination of 6 chemical factors (COD, NH₃-N, NO₃-N, Cr, Pb, Hg). However, when the main groups of the benthos, including the oligochaetes, were taken together, and a BPI (Biological Pollution Index) approach used, a correlation between the macroinvertebrate community and the combined chemical factors was noted.